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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/main/tools/deepvariant commit bf3bb5d5a1f442208f054523fbcf0be4cc366a35
author iuc
date Mon, 02 Feb 2026 12:34:14 +0000
parents 63b68fe4af85
children
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4:63b68fe4af85 5:fd52f65372c9
1 <tool id='deepvariant' name='DeepVariant' version='@TOOL_VERSION@+galaxy@SUFFIX_VERSION@' profile='20.01'> 1 <tool id='deepvariant' name='DeepVariant' version='@TOOL_VERSION@+galaxy@SUFFIX_VERSION@' profile='@PROFILE@'>
2 <description>deep learning-based variant caller</description> 2 <description>deep learning-based variant caller</description>
3 <macros> 3 <macros>
4 <import>macros.xml</import> 4 <import>macros.xml</import>
5 </macros> 5 </macros>
6 <expand macro='edam_ontology' /> 6 <expand macro='edam_ontology' />
9 ln -s '${reads}' reads_alignment.bam 9 ln -s '${reads}' reads_alignment.bam
10 && ln -s '${reads.metadata.bam_index}' reads_alignment.bam.bai 10 && ln -s '${reads.metadata.bam_index}' reads_alignment.bam.bai
11 #if $regions_conditional.regions_option == 'bed' 11 #if $regions_conditional.regions_option == 'bed'
12 && ln -s '${regions_conditional.bed_file}' region.bed 12 && ln -s '${regions_conditional.bed_file}' region.bed
13 #end if 13 #end if
14 #if $par_regions_bed
15 && ln -s '${par_regions_bed}' par_regions.bed
16 #end if
17 #set $logging_dir_value = None
18 #if $create_runtime_report
19 #set $logging_dir_value = 'logging'
20 && mkdir -p '$logging_dir_value'
21 #end if
14 #if $reference_genome.source == 'history': 22 #if $reference_genome.source == 'history':
15 #set $ref_genome = 'reference.fasta' 23 #set $ref_genome = 'reference.fasta'
16 && ln -s -f '${reference_genome.history_item}' $ref_genome 24 && ln -s -f '${reference_genome.history_item}' $ref_genome
17 && samtools faidx $ref_genome 25 && samtools faidx $ref_genome
18 #else: 26 #else:
19 #set $ref_genome = $reference_genome.index.fields.path 27 #set $ref_genome = $reference_genome.index.fields.path
20 #end if 28 #end if
21 && run_deepvariant 29 && run_deepvariant
22 --model_type=$model_type 30 --model_type=$model_type
23 --ref=$ref_genome 31 --ref=$ref_genome
24 --reads=reads_alignment.bam 32 --reads='reads_alignment.bam'
33 #if $sample_name
34 --sample_name '$sample_name'
35 #end if
25 --output_vcf='./output.vcf.gz' 36 --output_vcf='./output.vcf.gz'
26 #if $output_gvcf 37 #if $output_gvcf
27 --output_gvcf='./output.g.vcf.gz' 38 --output_gvcf='./output.g.vcf.gz'
28 #end if 39 #end if
29 #if $regions_conditional.regions_option == 'region' 40 #if $regions_conditional.regions_option == 'region'
30 --regions $regions_conditional.region_literal 41 --regions '$regions_conditional.region_literal'
31 #else if $regions_conditional.regions_option == 'bed' 42 #else if $regions_conditional.regions_option == 'bed'
32 --regions region.bed 43 --regions 'region.bed'
33 #end if 44 #end if
34 ##--call_variants_extra_args="use_openvino=true" ## Setting this will use OpenVINO on Intel CPUs, which empirically reduces call_variants runtime by 15%-25%. 45 --disable_small_model=$disable_small_model
46 #if $haploid_contigs
47 --haploid_contigs='$haploid_contigs'
48 #end if
49 #if $par_regions_bed
50 --par_regions_bed='par_regions.bed'
51 #end if
52 #if $logging_dir_value
53 --logging_dir='$logging_dir_value'
54 #end if
55 #if $report_title
56 --report_title='$report_title'
57 #end if
58 --runtime_report=$create_runtime_report
59 #if $make_examples_extra_args
60 --make_examples_extra_args='$make_examples_extra_args'
61 #end if
62 #if $call_variants_extra_args
63 --call_variants_extra_args='$call_variants_extra_args'
64 #end if
65 #if $postprocess_variants_extra_args
66 --postprocess_variants_extra_args='$postprocess_variants_extra_args'
67 #end if
68 $vcf_stats_report
35 --num_shards=\${GALAXY_SLOTS:-2} 69 --num_shards=\${GALAXY_SLOTS:-2}
36 && gunzip './output.vcf.gz' 70 && gunzip './output.vcf.gz'
37 #if $output_gvcf 71 #if $output_gvcf
38 && gunzip './output.g.vcf.gz' 72 && gunzip './output.g.vcf.gz'
39 #end if 73 #end if
55 <when value="history"> 89 <when value="history">
56 <param name="history_item" type="data" format="fasta" label="Reference genome" help="A reference genome in FASTA format" /> 90 <param name="history_item" type="data" format="fasta" label="Reference genome" help="A reference genome in FASTA format" />
57 </when> 91 </when>
58 </conditional> 92 </conditional>
59 <param argument="--reads" type="data" format="bam" label="BAM file" help="An aligned reads file in BAM format. The reads must be aligned to the reference genome" /> 93 <param argument="--reads" type="data" format="bam" label="BAM file" help="An aligned reads file in BAM format. The reads must be aligned to the reference genome" />
94 <param argument="--sample_name" type="text" optional="true" label="Sample name" help="Sample name to use instead of the SM tag in the BAM header. Example: NA12878" />
60 <param argument="--model_type" type="select" label="Model type" help="Type of model to use for variant calling"> 95 <param argument="--model_type" type="select" label="Model type" help="Type of model to use for variant calling">
61 <option value="WGS">WGS: Illumina whole genome sequencing</option> 96 <option value="WGS">WGS: Illumina whole genome sequencing</option>
62 <option value="WES">WES: Illumina whole exome sequencing</option> 97 <option value="WES">WES: Illumina whole exome sequencing</option>
63 <option value="PACBIO">PacBio HiFi</option> 98 <option value="PACBIO">PacBio HiFi</option>
64 <option value="HYBRID_PACBIO_ILLUMINA">Hybrid PacBio HiFi-Illumina</option> 99 <option value="HYBRID_PACBIO_ILLUMINA">Hybrid PacBio HiFi-Illumina</option>
86 <when value="bed"> 121 <when value="bed">
87 <param name="bed_file" argument="--regions" type="data" format="bed" label="BED file" help="The BED should the store genomic regions of interest" /> 122 <param name="bed_file" argument="--regions" type="data" format="bed" label="BED file" help="The BED should the store genomic regions of interest" />
88 </when> 123 </when>
89 </conditional> 124 </conditional>
90 <param argument="--output_gvcf" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Generate genomic VCF (gVCF) output" help="The key difference between a regular VCF and a gVCF is that the gVCF has records for all sites, whether there is a variant call there or not. The goal is to have every site represented in the file in order to do joint analysis of a cohort in subsequent steps" /> 125 <param argument="--output_gvcf" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Generate genomic VCF (gVCF) output" help="The key difference between a regular VCF and a gVCF is that the gVCF has records for all sites, whether there is a variant call there or not. The goal is to have every site represented in the file in order to do joint analysis of a cohort in subsequent steps" />
126 <section name="advanced_options" title="Advanced options" expanded="false">
127 <param argument="--disable_small_model" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Disable small model" help="Disable the use of the small model to call variants during make_examples." />
128 <param argument="--haploid_contigs" type="text" optional="true" label="Haploid contigs" help="Comma-separated list of non-autosomal chromosomes. Example: chrX,chrY" />
129 <param argument="--par_regions_bed" type="data" format="bed" optional="true" label="PAR regions BED file" help="BED file of pseudoautosomal regions." />
130 <param argument="--report_title" type="text" optional="true" label="Report title" help="Title for the VCF stats report (HTML). Example: NA12878 DeepVariant report" />
131 <param argument="--vcf_stats_report" type="boolean" truevalue="--vcf_stats_report=True" falsevalue="--vcf_stats_report=False" checked="False" label="Create VCF stats report (HTML)" help="Output a visual report (HTML) of statistics about the output VCF." />
132 <param name="create_runtime_report" argument="--runtime_report" type="boolean" truevalue="True" falsevalue="False" checked="False" label="Create runtime report" help="Output make_examples runtime metrics and create a visual runtime report." />
133 </section>
134 <section name="expert_options" title="Expert options (may increase runtime and disk usage)" expanded="false">
135 <param argument="--make_examples_extra_args" type="text" optional="true" label="make_examples extra args" help="Comma-separated flag_name=flag_value for make_examples.py. Example: min_base_quality=10,min_mapping_quality=5" />
136 <param argument="--call_variants_extra_args" type="text" optional="true" label="call_variants extra args" help="Comma-separated flag_name=flag_value for call_variants.py. Example: allow_empty_examples=true,batch_size=1024" />
137 <param argument="--postprocess_variants_extra_args" type="text" optional="true" label="postprocess_variants extra args" help="Comma-separated flag_name=flag_value for postprocess_variants.py. Example: cnn_homref_call_min_gq=20.0" />
138 </section>
91 </inputs> 139 </inputs>
92 <outputs> 140 <outputs>
93 <data name="vcf_file" format="vcf" from_work_dir="output.vcf" label="${tool.name} on ${on_string}: VCF file"/> 141 <data name="vcf_file" format="vcf" from_work_dir="output.vcf" label="${tool.name} on ${on_string}: VCF file"/>
94 <data name="html_report" format="html" from_work_dir="output.visual_report.html" label="${tool.name} on ${on_string}: HTML report"/> 142 <data name="html_report" format="html" from_work_dir="output.visual_report.html" label="${tool.name} on ${on_string}: HTML report">
143 <filter>advanced_options['vcf_stats_report']</filter>
144 </data>
145 <data name="runtime_report" format="html" from_work_dir="logging/make_examples_runtime_by_region_report.html" label="${tool.name} on ${on_string}: runtime report">
146 <filter>advanced_options['create_runtime_report']</filter>
147 </data>
95 <data name="gvcf_file" format="vcf" from_work_dir="output.g.vcf" label="${tool.name} on ${on_string}: gVCF file"> 148 <data name="gvcf_file" format="vcf" from_work_dir="output.g.vcf" label="${tool.name} on ${on_string}: gVCF file">
96 <filter>output_gvcf</filter> 149 <filter>output_gvcf</filter>
97 </data> 150 </data>
98 </outputs> 151 </outputs>
99 <tests> 152 <tests>
106 <param name="model_type" value="WGS"/> 159 <param name="model_type" value="WGS"/>
107 <param name="output_gvcf" value="False"/> 160 <param name="output_gvcf" value="False"/>
108 <conditional name="regions_conditional"> 161 <conditional name="regions_conditional">
109 <param name="regions_option" value="disabled"/> 162 <param name="regions_option" value="disabled"/>
110 </conditional> 163 </conditional>
111 <output name="vcf_file" file="output.vcf" ftype="vcf"> 164 <section name="advanced_options">
112 <assert_contents> 165 <param name="vcf_stats_report" value="True"/>
113 <has_text text="##fileformat=VCFv4.2"/> 166 <param name="report_title" value="Test Report Title"/>
114 <has_size value="2478" delta="10"/> 167 </section>
115 </assert_contents> 168 <output name="vcf_file" ftype="vcf">
116 </output> 169 <assert_contents>
117 <output name="html_report" file="report.html" ftype="html"> 170 <has_text text="##fileformat=VCFv4.2"/>
118 <assert_contents> 171 <has_text text="#CHROM"/>
119 <has_size value="23176" delta="100"/> 172 </assert_contents>
173 </output>
174 <output name="html_report" ftype="html">
175 <assert_contents>
176 <is_valid_xml />
177 <has_n_lines n="34" delta="10" />
178 <has_text text="Test Report Title"/>
120 </assert_contents> 179 </assert_contents>
121 </output> 180 </output>
122 </test> 181 </test>
123 <!-- Test region literal option--> 182 <!-- Test region literal option-->
124 <test expect_num_outputs="2"> 183 <test expect_num_outputs="2">
130 <param name="model_type" value="WGS"/> 189 <param name="model_type" value="WGS"/>
131 <conditional name="regions_conditional"> 190 <conditional name="regions_conditional">
132 <param name="regions_option" value="region"/> 191 <param name="regions_option" value="region"/>
133 <param name="region_literal" value="K03455:1-2669"/> 192 <param name="region_literal" value="K03455:1-2669"/>
134 </conditional> 193 </conditional>
135 <output name="vcf_file" ftype="vcf"> 194 <section name="advanced_options">
136 <assert_contents> 195 <param name="vcf_stats_report" value="True"/>
137 <has_text text="##fileformat=VCFv4.2"/> 196 </section>
138 <has_size value="1843" delta="10"/> 197 <output name="vcf_file" ftype="vcf">
139 </assert_contents> 198 <assert_contents>
140 </output> 199 <has_text text="#CHROM"/>
141 <output name="html_report" ftype="html"> 200 <has_text text="##fileformat=VCFv4.2"/>
142 <assert_contents> 201 </assert_contents>
143 <has_size value="18894" delta="100"/> 202 </output>
203 <output name="html_report" ftype="html">
204 <assert_contents>
205 <is_valid_xml />
206 <has_n_lines n="34" delta="10" />
207 <has_text text="Variant types"/>
144 </assert_contents> 208 </assert_contents>
145 </output> 209 </output>
146 </test> 210 </test>
147 <!-- Test region bed option--> 211 <!-- Test region bed option-->
148 <test expect_num_outputs="2"> 212 <test expect_num_outputs="2">
154 <param name="model_type" value="WGS"/> 218 <param name="model_type" value="WGS"/>
155 <conditional name="regions_conditional"> 219 <conditional name="regions_conditional">
156 <param name="regions_option" value="bed"/> 220 <param name="regions_option" value="bed"/>
157 <param name="bed_file" value="region.bed" ftype="bed"/> 221 <param name="bed_file" value="region.bed" ftype="bed"/>
158 </conditional> 222 </conditional>
159 <output name="vcf_file" ftype="vcf"> 223 <section name="advanced_options">
160 <assert_contents> 224 <param name="vcf_stats_report" value="True"/>
161 <has_text text="##fileformat=VCFv4.2"/> 225 </section>
162 <has_size value="1843" delta="10"/> 226 <output name="vcf_file" ftype="vcf">
163 </assert_contents> 227 <assert_contents>
164 </output> 228 <has_text text="#CHROM"/>
165 <output name="html_report" ftype="html"> 229 <has_text text="##fileformat=VCFv4.2"/>
166 <assert_contents> 230 </assert_contents>
167 <has_size value="18894" delta="100"/> 231 </output>
232 <output name="html_report" ftype="html">
233 <assert_contents>
234 <is_valid_xml />
235 <has_n_lines n="34" delta="10" />
236 <has_text text="Variant types"/>
168 </assert_contents> 237 </assert_contents>
169 </output> 238 </output>
170 </test> 239 </test>
171 <!-- Test gvcf output option--> 240 <!-- Test gvcf output option-->
172 <test expect_num_outputs="3"> 241 <test expect_num_outputs="3">
179 <param name="output_gvcf" value="True"/> 248 <param name="output_gvcf" value="True"/>
180 <conditional name="regions_conditional"> 249 <conditional name="regions_conditional">
181 <param name="regions_option" value="region"/> 250 <param name="regions_option" value="region"/>
182 <param name="region_literal" value="K03455:1-2669"/> 251 <param name="region_literal" value="K03455:1-2669"/>
183 </conditional> 252 </conditional>
184 <output name="vcf_file" ftype="vcf"> 253 <section name="advanced_options">
185 <assert_contents> 254 <param name="vcf_stats_report" value="True"/>
186 <has_text text="##fileformat=VCFv4.2"/> 255 </section>
187 <has_size value="1843" delta="10"/> 256 <output name="vcf_file" ftype="vcf">
188 </assert_contents> 257 <assert_contents>
189 </output> 258 <has_text text="#CHROM"/>
190 <output name="gvcf_file" file="output.g.vcf" ftype="vcf"> 259 <has_text text="##fileformat=VCFv4.2"/>
191 <assert_contents> 260 </assert_contents>
192 <has_text text="##fileformat=VCFv4.2"/> 261 </output>
193 <has_size value="3192" delta="10" /> 262 <output name="gvcf_file" ftype="vcf">
194 </assert_contents> 263 <assert_contents>
195 </output> 264 <has_text text="#CHROM"/>
196 <output name="html_report" ftype="html"> 265 <has_text text="##fileformat=VCFv4.2"/>
197 <assert_contents> 266 </assert_contents>
198 <has_size value="18894" delta="100"/> 267 </output>
268 <output name="html_report" ftype="html">
269 <assert_contents>
270 <is_valid_xml />
271 <has_n_lines n="34" delta="10" />
272 <has_text text="Variant types"/>
199 </assert_contents> 273 </assert_contents>
200 </output> 274 </output>
201 </test> 275 </test>
202 <!-- Test CRAM format input--> 276 <!-- Test CRAM format input-->
203 <test expect_num_outputs="2"> 277 <test expect_num_outputs="2">
208 <param name="reads" value="reads.cram"/> 282 <param name="reads" value="reads.cram"/>
209 <param name="model_type" value="WGS"/> 283 <param name="model_type" value="WGS"/>
210 <conditional name="regions_conditional"> 284 <conditional name="regions_conditional">
211 <param name="regions_option" value="disabled"/> 285 <param name="regions_option" value="disabled"/>
212 </conditional> 286 </conditional>
213 <output name="vcf_file" ftype="vcf"> 287 <section name="advanced_options">
214 <assert_contents> 288 <param name="vcf_stats_report" value="True"/>
215 <has_text text="##fileformat=VCFv4.2"/> 289 </section>
216 <has_size value="2478"/> 290 <output name="vcf_file" ftype="vcf">
217 </assert_contents> 291 <assert_contents>
218 </output> 292 <has_text text="#CHROM"/>
219 <output name="html_report" ftype="html"> 293 <has_text text="##fileformat=VCFv4.2"/>
220 <assert_contents> 294 </assert_contents>
221 <has_size value="23176" delta="100"/> 295 </output>
296 <output name="html_report" ftype="html">
297 <assert_contents>
298 <is_valid_xml />
299 <has_n_lines n="34" delta="10" />
300 <has_text text="Variant types"/>
222 </assert_contents> 301 </assert_contents>
223 </output> 302 </output>
224 </test> 303 </test>
225 <!-- Test indexed reference format input--> 304 <!-- Test indexed reference format input-->
226 <test expect_num_outputs="2"> 305 <test expect_num_outputs="2">
231 <param name="reads" value="reads.bam"/> 310 <param name="reads" value="reads.bam"/>
232 <param name="model_type" value="WGS"/> 311 <param name="model_type" value="WGS"/>
233 <conditional name="regions_conditional"> 312 <conditional name="regions_conditional">
234 <param name="regions_option" value="disabled"/> 313 <param name="regions_option" value="disabled"/>
235 </conditional> 314 </conditional>
236 <output name="vcf_file" ftype="vcf"> 315 <section name="advanced_options">
237 <assert_contents> 316 <param name="vcf_stats_report" value="True"/>
238 <has_text text="##fileformat=VCFv4.2"/> 317 </section>
239 <has_size value="2478"/> 318 <output name="vcf_file" ftype="vcf">
240 </assert_contents> 319 <assert_contents>
241 </output> 320 <has_text text="#CHROM"/>
242 <output name="html_report" ftype="html"> 321 <has_text text="##fileformat=VCFv4.2"/>
243 <assert_contents> 322 </assert_contents>
244 <has_size value="23176" delta="100"/> 323 </output>
324 <output name="html_report" ftype="html">
325 <assert_contents>
326 <is_valid_xml />
327 <has_n_lines n="34" delta="10" />
328 <has_text text="Variant types"/>
329 </assert_contents>
330 </output>
331 </test>
332 <!-- Test runtime report output-->
333 <test expect_num_outputs="3">
334 <conditional name="reference_genome">
335 <param name="source" value="history"/>
336 <param name="history_item" value="reference.fasta"/>
337 </conditional>
338 <param name="reads" value="reads.bam"/>
339 <param name="model_type" value="WGS"/>
340 <conditional name="regions_conditional">
341 <param name="regions_option" value="disabled"/>
342 </conditional>
343 <section name="advanced_options">
344 <param name="vcf_stats_report" value="True"/>
345 <param name="create_runtime_report" value="True"/>
346 </section>
347 <output name="vcf_file" ftype="vcf">
348 <assert_contents>
349 <has_text text="#CHROM"/>
350 <has_text text="##fileformat=VCFv4.2"/>
351 </assert_contents>
352 </output>
353 <output name="html_report" ftype="html">
354 <assert_contents>
355 <is_valid_xml />
356 <has_n_lines n="34" delta="10" />
357 <has_text text="Variant types"/>
358 </assert_contents>
359 </output>
360 <output name="runtime_report" ftype="html">
361 <assert_contents>
362 <is_valid_xml />
363 <has_text text="Overall runtime"/>
364 </assert_contents>
365 </output>
366 </test>
367 <!-- Test haploid contigs and PAR regions BED-->
368 <test expect_num_outputs="2">
369 <conditional name="reference_genome">
370 <param name="source" value="history"/>
371 <param name="history_item" value="reference.fasta"/>
372 </conditional>
373 <param name="reads" value="reads.bam"/>
374 <param name="model_type" value="WGS"/>
375 <conditional name="regions_conditional">
376 <param name="regions_option" value="disabled"/>
377 </conditional>
378 <section name="advanced_options">
379 <param name="vcf_stats_report" value="True"/>
380 <param name="haploid_contigs" value="K03455"/>
381 <param name="par_regions_bed" value="phix174.par_regions.bed" ftype="bed"/>
382 </section>
383 <output name="vcf_file" ftype="vcf">
384 <assert_contents>
385 <has_text text="#CHROM"/>
386 <has_text text="##fileformat=VCFv4.2"/>
387 </assert_contents>
388 </output>
389 <output name="html_report" ftype="html">
390 <assert_contents>
391 <is_valid_xml />
392 <has_n_lines n="34" delta="10" />
393 <has_text text="Variant types"/>
394 </assert_contents>
395 </output>
396 </test>
397 <!-- Test expert options extra-args-->
398 <test expect_num_outputs="2">
399 <conditional name="reference_genome">
400 <param name="source" value="history"/>
401 <param name="history_item" value="reference.fasta"/>
402 </conditional>
403 <param name="reads" value="reads.bam"/>
404 <param name="model_type" value="WGS"/>
405 <conditional name="regions_conditional">
406 <param name="regions_option" value="disabled"/>
407 </conditional>
408 <section name="advanced_options">
409 <param name="vcf_stats_report" value="True"/>
410 </section>
411 <section name="expert_options">
412 <param name="make_examples_extra_args" value="min_base_quality=10"/>
413 <param name="call_variants_extra_args" value="allow_empty_examples=true"/>
414 <param name="postprocess_variants_extra_args" value="cnn_homref_call_min_gq=20.0"/>
415 </section>
416 <output name="vcf_file" ftype="vcf">
417 <assert_contents>
418 <has_text text="#CHROM"/>
419 <has_text text="##fileformat=VCFv4.2"/>
420 </assert_contents>
421 </output>
422 <output name="html_report" ftype="html">
423 <assert_contents>
424 <is_valid_xml />
425 <has_n_lines n="34" delta="10" />
426 <has_text text="Variant types"/>
245 </assert_contents> 427 </assert_contents>
246 </output> 428 </output>
247 </test> 429 </test>
248 </tests> 430 </tests>
249 <help><![CDATA[ 431 <help><![CDATA[
252 434
253 **Purpose** 435 **Purpose**
254 436
255 DeepVariant is a deep learning-based variant caller that takes aligned reads (in BAM or CRAM format), produces pileup image tensors from them, classifies each tensor using a convolutional neural network, and finally reports the results in a standard VCF or gVCF file. 437 DeepVariant is a deep learning-based variant caller that takes aligned reads (in BAM or CRAM format), produces pileup image tensors from them, classifies each tensor using a convolutional neural network, and finally reports the results in a standard VCF or gVCF file.
256 438
439 DeepVariant runs a pipeline of three steps: **make_examples**, **call_variants**, and **postprocess_variants**. The **Expert options** section exposes extra-args fields for each step. Use these only with parameters that are accepted by the corresponding DeepVariant binary (see `run_deepvariant --helpfull` and the subcommand help, e.g. `/opt/deepvariant/bin/make_examples --helpfull` in the container).
440
257 DeepVariant supports germline variant-calling in diploid organisms. 441 DeepVariant supports germline variant-calling in diploid organisms.
258 442
259 - NGS (Illumina) data for either a `whole genome <https://github.com/google/deepvariant/blob/r1.2/docs/deepvariant-case-study.md>`_ or `whole exome <https://github.com/google/deepvariant/blob/r1.2/docs/deepvariant-exome-case-study.md>`_. 443 - NGS (Illumina) data for either a `whole genome <https://github.com/google/deepvariant/blob/r1.9/docs/deepvariant-case-study.md>`_ or `whole exome <https://github.com/google/deepvariant/blob/r1.9/docs/deepvariant-exome-case-study.md>`_.
260 - PacBio HiFi data, see the `PacBio case study <https://github.com/google/deepvariant/blob/r1.2/docs/deepvariant-pacbio-model-case-study.md>`_. 444 - PacBio HiFi data, see the `PacBio case study <https://github.com/google/deepvariant/blob/r1.9/docs/deepvariant-pacbio-model-case-study.md>`_.
261 - Hybrid PacBio HiFi + Illumina WGS, see the `hybrid case study <https://github.com/google/deepvariant/blob/r1.2/docs/deepvariant-hybrid-case-study.md>`_. 445 - Hybrid PacBio HiFi + Illumina WGS, see the `hybrid case study <https://github.com/google/deepvariant/blob/r1.9/docs/deepvariant-hybrid-case-study.md>`_.
262 446
263 Please also note: 447 Please also note:
264 448
265 For somatic data or any other samples where the genotypes go beyond two copies of DNA, DeepVariant will not work out of the box because the only genotypes supported are hom-alt, het, and hom-ref. 449 For somatic data or any other samples where the genotypes go beyond two copies of DNA, DeepVariant will not work out of the box because the only genotypes supported are hom-alt, het, and hom-ref.
266 450